[Chimera-users] Advice on SASA

[George Tzotzos]

I have a couple of questions on Chimera’s implementation of SASA. First, I’ll try to explain briefly my problem and then ask the questions.

My protein is a homodimer. There exist 3 X-ray structures of the protein in complex with serendipitous ligand as well as in complex with biological ones. The ligands bind at the interface between the two chains of the homodimer. It is not clear whether dimer formation is a crystallographic artefact. Biochemical experiments are likewise inconclusive. It has been argued that the biological ligands may stabilise the formation of the dimer. Furthermore, it has been argued that upon ligand binding some of the interface residues become buried. 

I’ve conducted extensive MD simulations with and without the biological ligands. I would like to test whether ligand binding has an effect on the SASA of the interface residues. 

1. Can I restrict measurement of SASA to selected residues only? In other words, can I use a mask specifying the residues of interest?
2. From the documentation, I understand that the Chimera implementation of SASA is applied on single pdb structures and not on trajectories. If I use representative structures from MD clusters, should I strip the ligand before measuring SASAs? 

Thank you in advance for your suggestions and apologies for the long-winded explanation. 

Best regards

George